Version 1.1 - January 2004
This new release has enhanced tools for aligning sequences and working with regulatory elements.
Version 1.0 - November 2003
Sockeye on the cover of the November 2003 Linux Journal. The screenshot shows a BLASTX comparison of the SARS Tor2 coronavirus genome against known proteins of other similar viruses. The user-configurability of 3D features made it simple to change the default behaviour to height-scaled in order to show relative BLASTX similarities, and to colour-code proteins to show functional similarity.
Version 0.8.4 - May 2003
Combine external local calculations, GFF and Ensembl data
Conserved regions (GFF data, vertical bars) identified by mLAGAN in 100 Kb regions upstream of the 5' end of the human CFTR gene (Ensembl data, yellow cylinder in left image), and orthologous genes for a 'zoo' of species. Results for each species are shown as a set of bars on a pale blue baseline, with bar height proportional to the similarity score. Orange and yellow cylinders are genes, green cylinders are exons; red hexagons are repeats (user-editable). The CFTR gene is on the forward strand; the similarity results overlap a gene on the reverse strand (see chr.7: 115,450,000..115,800,000; the GFF-to-Ensembl alignment shown is arbitrary to within a few hundred bases). The right image shows a popup menu giving all GFF fields for a similarity bar (highlighted), and both relative and absolute coordinates.
Combine external public calculations, GFF and Ensembl data
Conserved regions between human, mouse and rat CFTR genes, from Vista alignments. Ensembl FASTA sequences for mouse, rat and fugu genes were aligned against the Human Nov. 2002 base genome at the GenomeVista server. Human coordinates for conserved regions with >70% similarity over 100 bp were returned. For mouse and rat, results were saved as flat files that were converted to GFF with a custom Perl script. No hits were returned for Fugu. To display the GFF results in Sockeye, Mm_Hs_ and Rn_Hs_similarity features, with corresponding baseline features, were added to user_config.xml, and the GFF data were imported and added to the CFTR Ensembl human track. Ensembl mouse and rat data were added with 'between-query' ranges set to centre the CFTR genes on the human gene. The similarity bar set closer to the human gene is rat-human; the farther set is mouse-human. Features are as in the above figures. As above, popup menus give detailed information on a 3D feature.
Wide dynamic range
The 19.5K genes on the six C. elegans chromosomes, queried directly from Ensembl v12 into a Sockeye running with 512 MB of Java RAM. The second and third images show a dynamic Java3D mouse zoom-in. Popup menus show summary information on a selected gene; other popup menus (not shown) offer Web links to detailed Ensembl or NCBI information.
- Genes with more than one transcript are marked by a floating-ball 'flag'. Passing the mouse over a flag pops up a label with the gene name and the number of transcripts (not shown).
- A right-click on a gene or exon pops up a menu that lists all transcripts for the gene and offers links to detailed Web information (left figure). Checking a transcript in the list persistently highlights its exon set.
- A right-click on a multitranscript flag pops up an initial implementation of a 2D display of all transcripts for the gene (right figure). The 2D display is consistent with the highlighted exon sets in the two figures.
The black line is the genome centreline; the forward strand is above and the reverse strand is below. The pale purple blocks are CpG islands. (Feature shapes and colours are user-editable.)